Selecting Bioinformatic Tools for Public Health
Jared Johnson, PhD, MSc
April 8, 2025
Why do you need the tool?
What will be reported?
Who are you reporting to?
How will the tool be used?
Clinical vs surveillance
Frequency of reporting
What resources do you have?
Human resources (e.g., technical expertise)
Compute resources
Lab resources (e.g., sequencers)
Bioinformatic tools often have multiple functions / outputs
Clearly define what will be reported (e.g., AMR genes, phylogenetic tree, clade, etc.,)
Helps to avoid becoming overwhelmed or distracted
Who will receive the results?
How will the result be used?
Clinical vs Surveillance
Frequency of Reporting & Sample Size
Human Resources
Compute Resources
Available hardware and software
IT restrictions
Lab Resources
Institutions
CDC : MycoSNP, PHoeNIx, IRMA/MIRA
Broad : GATK, Terra, Cromwell, IGV, Picard, Pilon
Development Teams
Nextstrain : Nextclade, Auspice, Augur
Andersen Lab : Freyja, iVar
State Labs
UT PHL : Cecrete
WA PHL : BigBacter, VAPER, EPITOME, RECAPP, pre_mycosnp
Developers
Torsten Seemann : Prokka, Snippy, Shovill, Abricate, mlst
Ryan Wick : Unicycler, Bandage, Polypolish, Trycycler
Slack Channels
State Public Health Bioinformatics Workgroup (StaPH-B)
ChatGPT
8 tools
(no links)
(long vs short)
Copilot
3 tools
(with links)
Gemini
1 tool
(no links)
Essential Criteria
Ideal Criteria
Deadware - software or hardware that is no longer supported, maintained, or updated by its manufacturer.
Work in groups to complete the activity:
Ideal Criteria
Ideal Criteria
Ideal Criteria
Work in groups to complete the activity:
Questions
Q1. Which assembler would you choose?
Q2. What was your big take away from the activity?
Q3. Would you add anything to the lists of “Ideal” or “Essential” criteria?